Finally I sat down and went through the documents that describe how to upgrade from 5 to 6. I only have an handful users. I also have the posix/samba zimlets in use.
I followed the following documents:
- Optimizing 5.0 to 6.0 LDAP upgrade
- Managing Customized BDB configurations
- Installing custom ldap schema 6.0

Errors encountered:
While none of the ldap start command did work, in the end the upgrade completed successfully.

Things are running fine in 6.0.5 so far.
The only thing that did not work no more was Monitoring - Server Status
Some search in the forum gave me some hints.
The solution in my case was to switch from syslog to rsyslog in the service configuration.